Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions

<p>Abstract</p> <p>Background</p> <p>The information from different data sets experimented under different conditions may be inconsistent even though they are performed with the same research objectives. More than that, even when the data sets were generated from the same platform, the data agreement may be affected by the technical variation among the laboratories. In this case, it is necessary to use the combined data set after adjusting the differences between such data sets, for detecting the more reliable information.</p> <p>Results</p> <p>The proposed method combines data sets posterior to the discretization of data sets based on the ranks of the gene expression ratios, and the statistical method is applied to the combined data set for predictive gene selection. The efficiency of the proposed method was evaluated using five colon cancer related data sets, which were experimented using cDNA microarrays with different RNA sources, and one experiment utilized oligonucleotide arrays. NCI-60 cell lines data sets were used, which were performed with two different platforms of cDNA microarrays and Affymetrix HU6800 oligonucleotide arrays. The combined data set by the proposed method predicted the test data sets more accurately than the separated data sets did. The biological significant genes were detected from the combined data set, which were missed on the separated data sets.</p> <p>Conclusion</p> <p>By transforming gene expressions using ranks, the proposed method is not influenced by systematic bias among chips and normalization method. The method may be especially more useful to find predictive genes from data sets which have different scale in gene expressions.</p

Short-Term Effects of Combined Serial Casting and Botulinum Toxin Injection for Spastic Equinus in Ambulatory Children with Cerebral Palsy

PURPOSE: The purpose of this paper is to test the hypothesis that combination therapy of serial cast and botulinum toxin type A (BTX-A) injection can further enhance the effects of a BTX-A injection in ambulant children with cerebral palsy (CP) who have an equinus foot. MATERIALS AND METHODS: Children in group A (30 legs of 21 children) received a serial casting application after an injection of BTX-A, and children in group B (25 legs of 17 children) received only a BTX-A injection. Assessments were performed before the intervention and 1 month after the intervention. RESULTS: After the intervention, there were significant improvements in tone, dynamic spasticity, and passive range of motion (ROM) in both groups. However, the changes were greater in group A than in group B. Dimension D (standing) in Gross Motor Function Measure (GMFM)-66 was significantly improved in group A but not in group B. On the other hand, there were no significant changes in dimension E (walking, running, jumping) in GMFM-66 in either group. CONCLUSION: The results of our study suggest that a serial casting application after BTX-A injection can enhance the benefits of BTX-A injection in children with cerebral palsy.ope

Novel and simple transformation algorithm for combining microarray data sets

<p>Abstract</p> <p>Background</p> <p>With microarray technology, variability in experimental environments such as RNA sources, microarray production, or the use of different platforms, can cause bias. Such systematic differences present a substantial obstacle to the analysis of microarray data, resulting in inconsistent and unreliable information. Therefore, one of the most pressing challenges in the field of microarray technology is how to integrate results from different microarray experiments or combine data sets prior to the specific analysis.</p> <p>Results</p> <p>Two microarray data sets based on a 17k cDNA microarray system were used, consisting of 82 normal colon mucosa and 72 colorectal cancer tissues. Each data set was prepared from either total RNA or amplified mRNA, and the difference of RNA source between these two data sets was detected by ANOVA (Analysis of variance) model. A simple integration method was introduced which was based on the distributions of gene expression ratios among different microarray data sets. The method transformed gene expression ratios into the form of a reference data set on a gene by gene basis. Hierarchical clustering analysis, density and box plots, and mixture scores with correlation coefficients revealed that the two data sets were well intermingled, indicating that the proposed method minimized the experimental bias. In addition, any RNA source effect was not detected by the proposed transformation method. In the mixed data set, two previously identified subgroups of normal and tumor were well separated, and the efficiency of integration was more prominent in tumor groups than normal groups. The transformation method was slightly more effective when a data set with strong homogeneity in the same experimental group was used as a reference data set.</p> <p>Conclusion</p> <p>Proposed method is simple but useful to combine several data sets from different experimental conditions. With this method, biologically useful information can be detectable by applying various analytic methods to the combined data set with increased sample size.</p

Postoperative Spinal Epidural Hematoma: The Danger Caused by the Misuse of Thrombin-Containing Local Hemostatics

Study DesignRetrospective case-control study.PurposeTo examine the hypothesis that the misuse of thrombin-containing local hemostatics (TCLH) increases the risk of postoperative spinal epidural hematoma (POSEH).Overview of LiteratureMany studies have focused on hypocoagulability as a risk factor for POSEH. However, there are no prior reports on the increased risk of POSEH in hypercoagulable states.MethodsPosterior instrumented lumbar spine surgery cases over 2 consecutive years were divided into two groups: a study group (98 patients in whom TCLH was used) and a control group (176 patients in whom TCLH was not used). The excess TCLH matrix that was not associated with blood clot was not removed from the patients in the study group. The senior author decided whether to use TCLH or not. Suction drains were used in all patients. The demographics, coagulation-related factors, and intraoperative factors of the patients in the two groups were analyzed. The development of POSEH was compared between the two groups.ResultsThe two groups were homogenous in demographics (age and sex), coagulation-related factors (platelet count, prothrombin time, activated partial thromboplastin time, and platelet function analysis), and surgical factors (total blood loss, operation time, blood loss/10 minutes, number of fusion segments, posterolateral fusion/posterior lumbar interbody fusion, and virgin or revision surgery). POSEH developed more frequently in the patients in the study group than in those in the control group (14/98 patients, 14.3% vs. 3/176 patients, 1.7%, respectively; p=0.001; odds ratio, 17.1).ConclusionsTCLH causes blood clot not only at the edge of damaged vessels but also at the site of extravascular blood. Excess TCLH matrix not associated with blood clot at the epidural space can enhance POSEH development because early clotted hematomas do not drain through suction drains

Concomitant Laparoendoscopic Single-Site Surgery for Vesicolithotomy and Finger-Assisted Single-Port Transvesical Enucleation of the Prostate

Transurethral resection of the prostate is the most common surgery for benign prostatic hyperplasia. However, it doesn't work best for men with very large prostate and bladder stones. Herein we report our initial experience with concomitant laparoendoscopic single-site surgery and finger-assisted single-port transvesical enucleation of the prostate for the treatment of the condition

Prognostic Factors of Neurological Complications in Spinal Surgeries

Study Design Retrospective study. Purpose To determine prognostic factors of neurological complications (NCs) of posterior thoracolumbar surgeries. Overview of Literature There have been few reports on the prognosis of NCs according to the causes and treatment methods. Methods The subjects were 65 patients who had NCs for 19 years (1995–2013) after posterior thoracolumbar surgeries in Seoul Sacred Heart General Hospital. The degree of neurological injury was assessed using numeric scales as follows: G1, increased leg pain or sensory loss; G2, hemiparesis; G3, paraparesis; G4, cauda equine syndrome; and G5, complete paraplegia. The relative degree of neurological recovery was evaluated using four numeric scales as follows: Gr1, complete recovery; Gr2, almost complete recovery with residual sensory loss or numbness; Gr3, partial recovery with apparent neurological deficit; and Gr4, no recovery. The prognostic factors were investigated in terms of demographic and surgical variables that were available in a retrospective review. Results The causes were as follows: epidural hematoma (EH), 25 patients (38.5%); insufficient decompression and fusion, 14 patients (21.5%); mechanical injury, 11 patients (16.9%); insufficient discectomy, four patients (6.2%); and unknown, 11 patients (23.1%). The grade of neurological injury was as follows: G1, 11 patients (16.9%); G2, 34 patients (52.3%); G3, 15 patients (23.1%); G4, three patients (4.6%); and G5, two patients (3.1%). Thirteen patients received conservative treatment, and 52 underwent revision surgeries. Neurological recovery was as follows: Gr1, 21 patients (32.3%); Gr2, 17 patients (26.2%); Gr3, 20 patients (30.8%); and Gr4, seven patients (10.8%). The prognosis depended on the causes (p =0.041). The subgroup analysis of the revision group revealed a significant correlation between the degree of neurological recovery and the timing of revision, irrespective of causes (r =0.413, p =0.002). Conclusions The prognosis of NC depended on the causes. EH was the best and unknown was the worst prognostic factor. Revision should be performed as soon as possible for a better prognosis

Morphological changes of the lateral meniscus in end-stage lateral compartment osteoarthritis of the knee.

OBJECTIVE: The aim of this study was to evaluate the morphological changes of the lateral meniscus in end-stage lateral compartment osteoarthritis (OA) of the knee. METHODS: One hundred fifty-eight knee joints from 133 patients that subsequently underwent total knee joint arthroplasty from January 2008 to December 2009 were enrolled. There were 26 men and 107 women. Their ages ranged from 56 to 81 (mean 67.4 + 6.5 years). All study participants had complete obliteration of the lateral joint space identified by weight-bearing radiography. Meniscal position was assessed by measuring meniscal subluxation and meniscal height. The meniscal morphology was assessed using a modification of the whole-organ magnetic resonance imaging score (WORMS). The frequency of different meniscal morphology and their respective positions was calculated. RESULTS: The predominant type (42.4%, 53.8% and 52.5% in the anterior horn, mid-body and posterior horn, respectively) of abnormal meniscal morphology was a complete maceration/destruction or complete resection. The anterior horn of non-macerated lateral meniscus was more subluxed than that of the non-macerated medial meniscus in patients with lateral OA. CONCLUSION: This study suggests that the lateral meniscus in persons with end-stage lateral OA are mostly macerated or destroyed. Also, unlike isolated end-staged medial compartment OA, the anterior horn of the lateral meniscus in isolated end-stage lateral OA is commonly affected. Copyright 2011 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved

Factors affecting the long-term outcomes of idiopathic membranous nephropathy

Abstract Background We attempted to describe the clinical features and determine the factors associated with renal survival in idiopathic membranous nephropathy (iMN) patients with nephrotic syndrome (NS) and to determine the factors associated with spontaneous complete remission (sCR) and progression to NS in iMN patients with subnephrotic proteinuria. Methods This retrospective study involved 166 iMN patients with NS and 65 patients with subnephrotic proteinuria. The primary end point was a doubling of serum creatinine or initiation of dialysis. In patients with subnephrotic proteinuria, we determined the factors associated with sCR and factors associated with progression to NS. Results Remission of NS was achieved in 125 out of 166 patients (75.3%). Of those who reached remission, 26 patients (20.8%) experienced relapse that was followed by second remission. The relapse or persistence of proteinuria was associated with the primary end points (hazard ratio [HR] = 12.40, P = 0.037, HR = 173, P < 0.001, respectively). In patients with subnephrotic proteinuria, sCR occurred in 35.4% of the patients. The patients with sCR had lower proteinuria and serum creatinine levels and higher serum albumin concentrations at baseline. The serum albumin level at diagnosis was a prognostic factor for progression to NS (Odds ratio [OR] = 0.015, P < 0.001). Conclusions The occurrence of relapse or persistence of proteinuria had negative effects on renal survival in iMN patients with NS, and low serum albumin levels at baseline were associated with non-achievement of sCR and progression to NS